Comprehensive methylome and transcriptome profiling reveals specific biomarkers for bovine viral diarrhea virus persistent infection in calves

Background Persistently infected (PI) calves resulting from maternal Bovine viral diarrhea virus (BVDV) infection during early gestation are the main source of viral transmission and pose a serious threat to the sustainable production of herds. PI cattle appear clinically normal, elucidating the molecular-level alterations is critical for understanding their specific characteristics. Moreover, the identification of candidate biomarkers for diagnosing PI cattle will provide valuable insights to support effective strategies for the control and eventual eradication of BVDV. At the same time, few studies have focused on the mothers of PI calves (Trojan dam). Methods We integrated RNA-seq and reduced representation bisulfite sequencing (RRBS) to characterize the molecular features of PI calves and Trojan dams and identified DNA methylation biomarkers in PI calves. Results In this study, we found that both B cell and T cell receptor signaling pathways were less active in PI calves, along with a significantly reduced B cell proportion compared to normal calves. By integrating transcriptome and methylation data, we found that the elevated expression of MAPK13 and LSP1 in PI calves is potentially regulated by promoter methylation. Furthermore, we identified a potential ZBTB38–methylation–MAPK13 regulatory axis influencing downstream genes such as IL1B , KDR , FOSB , and PTGS2 , which may collectively impact the physiological state of PI calves. In Trojan dams and normal dams, we identified a total of eight genes potentially regulated by DNA methylation, including KLHL33 , KLRG1 , NQO2 and etc. By comparing PI calves with Trojan dams, normal calves, and normal dams, we identified a differentially methylated region (DMR) located in the PES1 gene that was specifically hypomethylated in PI calves but hypermethylated in the other groups, suggesting its potential as a candidate diagnostic biomarker for PI detection. Conclusion Our study revealed that the immune system of PI cattle is already compromised and identified a novel candidate diagnostic biomarker, providing a new perspective for the detection of PI cattle. In addition, we reveal that prenatal BVDV exposure induces persistent DNA methylation alterations in Trojan dams.